sphingomyelin (d18:1/20:2, d18:2/20:1, d16:1/22:2)* to sphingomyelin (d18:2/18:1)*

Numerator Metabolite

Metabolite Accession: GCST90199995
Name: sphingomyelin (d18:1/20:2, d18:2/20:1, d16:1/22:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Structure of sphingomyelin (d18:2/18:1)*
Metabolite Accession: GCST90200128
Name: sphingomyelin (d18:2/18:1)*
Hmdb Id: HMDB0001348
Super Pathway: NA
Sub Pathway: NA
Inchikey: LKQLRGMMMAHREN

Associated Genomic Regions

Region: rs102274

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Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
0.209
Position:
61557826
SE (Ratio):
0.012
Effect Allele:
C
Z-score (Ratio):
17.469
Reference Allele:
T
-log10(P):
-155.664
MAF:
0.340
Beta (Num):
0.184
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
-0.025
SE (Den):
0.015
No CNV overlap
rQTL cluster:
62
Reaction Distance:
NA
Closest Genes:
TMEM258 MYRF FEN1 FADS2 FADS1

Region: rs12878001

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Clumped rQTL variant

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SNP Summary

Chr:
14
Beta (Ratio):
0.168
Position:
64239629
SE (Ratio):
0.015
Effect Allele:
G
Z-score (Ratio):
11.042
Reference Allele:
T
-log10(P):
-63.599
MAF:
0.165
Beta (Num):
0.169
Novel Locus:
No
SE (Num):
0.019
Beta (Den):
9.62e-04
SE (Den):
0.019
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

Region: rs438568

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
0.136
Position:
12958687
SE (Ratio):
0.012
Effect Allele:
A
Z-score (Ratio):
11.559
Reference Allele:
G
-log10(P):
-69.490
MAF:
0.385
Beta (Num):
0.082
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
-0.054
SE (Den):
0.015
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism3[1]

Denominator Metabolite Explanation:

Sphingolipid metabolism3[1]

Ratio Explanation:

The ratio reflects the relative activity of desaturation in sphingomyelin species, influenced by FADS1/FADS2, which create polyunsaturated fatty acids incorporated into these lipids.4[1]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Reduced FADS1/FADS2 activity, indicated by the ratio, alters cell membrane composition and signaling, which may contribute to benign colon neoplasms and valvular heart disease.4[1], 5[2], 6[3], 7[4]

Phenotype Driver:

Gene-centric:FADS1/FADS2

Downloads

Download the full rQTL summary statistics file for this metabolite ratio. Data contains the loci listed here. For each SNP (chromosome, effect_allele, reference_allele, pos_name, position) these columns contain the summary statistics of the ratio (beta, pgain, pval, se, z), the numerator metabolite (beta_1, pval_1, n_iids_1, effect_allele_frequency_1, se_1, z_1) and the denominator metabolite (beta_2, pval_2, n_iids_2, effect_allele_frequency_2, se_2, z_2)

Download rQTL Data